Hal 9000 said:

Was the 2003 retconned out of existence? If the two are mutually exclusive, I'll take the Samurai Jack style cartoon any day.

Well, considering how many differences there are (namely Asajj Ventress dying in the original cartoon and being the main villain in the new show.) I think it's safe to say that either this new series either cancels out the old one or is meant to be standalone.

By the way, Mr. thunderclap, will you be keeping the plot of the pilot, or will you be using a storyline from the TV series?